Rapid Evolution of cis-Regulatory Architecture and Activity in the Drosophila Yellow Gene.

Abstract

In the last 10 years, an increasing number of case studies showed that changes in cis-regulatory elements, mainly enhancers, are one of the main causes of altered phenotypes, but the mechanisms underlying enhancer evolution remain to be elucidated. More specifically, what is the relationship between changes in enhancer sequence, transcription factor binding and activity? In this thesis, I used evolution of yellow enhancers among Drosophila species as a model to shed light onto how cis-regulatory architecture and activity change over time. I first identified the enhancer activities lying in the 5’ intergenic and intronic regions of yellow from six Drosophila species spanning the Drosophila evolutionary history, using a reporter gene assay. I found that yellow epidermal-cell and wing-vein, but not bristle enhancers, have different positions, with respect to the coding sequence, in different Drosophila species. This was the first systematic demonstration of altered enhancer position between species and suggested that enhancer position can be labile. Sequence comparisons failed to show any indication of translocation or duplication suggesting gradual compensatory changes in the transcription factor binding profiles of yellow enhancers is the likely mechanism underlying altered enhancer position. Subsequent subdivision of yellow 5’ intergenic and intronic regions showed a complex distribution of enhancer activities among sub-elements, where some drove expression in patterns that were not part of the expression pattern driven by the full region. Existence of such “cryptic” epidermal-cell enhancer activities suggests that yellow cis-regulatory regions were primed for facilitating the rapid evolutionary changes in the position and activities of this enhancer. Lastly, for the first time, I identified a large set of candidate transcription factors binding to yellow enhancers. This thesis shows that position and activity of yellow enhancers diverged rapidly among species, perhaps by taking advantage of the cryptic activities lying in the yellow cis-regulatory sequences. Further in vitro and in vivo tests validating the direct binding of the identified transcription factors on yellow enhancers and characterizing their functional effects on yellow expression among species can elucidate the evolutionary changes underlying altered position and activity of the particular yellow enhancers.